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New file with protein and protein-ligand interaction is added. #1292

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karolamik13
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I created new module which compute protein and protein-ligand interactions.
For protein-ligand interactions there are some additional requirements i.e. installation of Openbabel and PLIP.
There is also new function which after Openbabel installation can provide adding hydrogens to protein and ligand structures.

@jamesmkrieger
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It could be good to provide an option for adding hydrogens using PDBFixer too.

@karolamik13
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karolamik13 commented Feb 1, 2021 via email

@karolamik13
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All except adding PDBFixer is ready.

@jamesmkrieger
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Sounds good

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Everything looks good except for kwargs for interaction scores

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A few more minor things

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@jamesmkrieger jamesmkrieger self-requested a review February 4, 2021 10:39
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The scoring kwargs thing still needs fixing

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@jamesmkrieger jamesmkrieger added the Enhancement Improvement to an already-existing feature. label Sep 15, 2021
aa_acceptor_atom = atoms.getNames()[k[2]]+'_'+str(k[2])
aa_acceptor_chain = atoms.getChids()[k[2]]

HBs_list.append([aa_donor, aa_donor_atom, aa_donor_chain, aa_acceptor, aa_acceptor_atom,
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Perhaps you could order it this way round like in the second part of the SHEET header records of the PDB (taken from line 1578 of 2tbv):

O LEU A 263 N VAL A 103

See http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#SHEET

This would include splitting resnum and resname, which is probably a good idea anyway.

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